diff --git a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoLaunchConfigurationDelegate.java b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoLaunchConfigurationDelegate.java
index 9f12fec..572bb8a 100644
--- a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoLaunchConfigurationDelegate.java
+++ b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoLaunchConfigurationDelegate.java
@@ -17,14 +17,18 @@
 package org.apache.geronimo.st.v30.core;
 
 import java.io.File;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
 import org.apache.geronimo.st.v30.core.internal.Messages;
 import org.apache.geronimo.st.v30.core.internal.Trace;
+import org.apache.geronimo.st.v30.core.util.ConfigSubstitutionsHelper;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
@@ -139,35 +143,34 @@
         boolean managedApplicationStart = server.getServerDelegate().isManageApplicationStart();        
         Trace.trace(Trace.INFO, "GeronimoLaunchConfigurationDelegate: manageApplicationStart:=" + managedApplicationStart, Activator.traceCore);
         
-        int params = 0;
+        List<String> params = new ArrayList<String>(6);
+        
+        GeronimoServerDelegate serverDelegate = server.getServerDelegate();
+
+        params.add("-Dorg.apache.geronimo.config.substitution.prefix=gep.");
+        params.add("-Dgep." + ConfigSubstitutionsHelper.PORT_OFFSET + "=" + serverDelegate.getPortOffset());
+        params.add("-Dgep." + ConfigSubstitutionsHelper.HTTP_PORT + "=" + serverDelegate.getHTTPPort());
+        params.add("-Dgep." + ConfigSubstitutionsHelper.NAMING_PORT + "=" + serverDelegate.getRMINamingPort());
+        
         Set<String> deletedConfigs = server.getDeletedConfigIds();
         if (!deletedConfigs.isEmpty()) {
-            params++;
+            params.add(toString("-Dgeronimo.removedArtifactList=", deletedConfigs));
         } 
         
-        Set<String> modifiedConfigs = null;        
         if (managedApplicationStart) {
-            modifiedConfigs = server.getModifiedConfigIds();
+            Set<String> modifiedConfigs = server.getModifiedConfigIds();
             if (!modifiedConfigs.isEmpty()) {
-                params++;
+                params.add(toString("-Dgeronimo.loadOnlyConfigList=", modifiedConfigs));
             }
-        } else {
-            modifiedConfigs = Collections.emptySet();
         }
-        
-        if (params > 0) {
-            String[] newJvmArguments = new String[jvmArguments.length + params];
-            System.arraycopy(jvmArguments, 0, newJvmArguments, 0, jvmArguments.length);
-            int index = jvmArguments.length;
-            if (!modifiedConfigs.isEmpty()) {
-                newJvmArguments[index] = toString("-Dgeronimo.loadOnlyConfigList=", modifiedConfigs);
-                index++;
-            }
-            if (!deletedConfigs.isEmpty()) {
-                newJvmArguments[index] = toString("-Dgeronimo.removedArtifactList=", deletedConfigs);
-            }
-            jvmArguments = newJvmArguments;
+                
+        int size = params.size();
+        String[] newJvmArguments = new String[jvmArguments.length + size];
+        System.arraycopy(jvmArguments, 0, newJvmArguments, 0, jvmArguments.length);
+        for (int i = 0; i < size; i++) {
+            newJvmArguments[jvmArguments.length + i] = params.get(i);
         }
+        jvmArguments = newJvmArguments;
         
         return jvmArguments;
     }
diff --git a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoRuntimeDelegate.java b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoRuntimeDelegate.java
index 67b720e..d10183f 100644
--- a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoRuntimeDelegate.java
+++ b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoRuntimeDelegate.java
@@ -23,9 +23,7 @@
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.Properties;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
@@ -51,8 +49,6 @@
 
     private static final String PROP_VM_INSTALL_ID = "vm-install-id";
 
-    public static final String SERVER_INSTANCE_PROPERTIES = "geronimo_server_instance_properties";
-
     public static final String RUNTIME_SOURCE= "runtime.source";
 
     public static final int NO_IMAGE = 0;
@@ -164,15 +160,12 @@
      * @see org.apache.geronimo.st.v30.core.IGeronimoRuntime#getRuntimeSourceLocation()
      */
     public IPath getRuntimeSourceLocation() {
-        String source = (String) getServerInstanceProperties().get(RUNTIME_SOURCE);
-        if (source != null) {
-            return new Path(source);
-        }
-        return null;
+        String source = getAttribute(RUNTIME_SOURCE, (String) null);
+        return (source != null) ? new Path(source) : null;
     }
 
     public void setRuntimeSourceLocation(String path) {
-        setInstanceProperty(RUNTIME_SOURCE, path);
+        setAttribute(RUNTIME_SOURCE, path);
     }
 
     /**
@@ -285,38 +278,6 @@
     }
 
     /**
-     * @return
-     */
-    public Map getServerInstanceProperties() {
-        return getAttribute(SERVER_INSTANCE_PROPERTIES, new HashMap());
-    }
-
-    /**
-     * @param map
-     */
-    public void setServerInstanceProperties(Map map) {
-        setAttribute(SERVER_INSTANCE_PROPERTIES, map);
-    }
-
-    /**
-     * @param name
-     * @return
-     */
-    public String getInstanceProperty(String name) {
-        return(String) getServerInstanceProperties().get(name);
-    }
-
-    /**
-     * @param name
-     * @param value
-     */
-    public void setInstanceProperty(String name, String value) {
-        Map map = getServerInstanceProperties();
-        map.put(name, value);
-        setServerInstanceProperties(map);
-    }
-
-    /**
      * @param vmInstall
      */
     public void setVMInstall(IVMInstall vmInstall) {
diff --git a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerBehaviourDelegate.java b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerBehaviourDelegate.java
index 8067450..1f9e349 100644
--- a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerBehaviourDelegate.java
+++ b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerBehaviourDelegate.java
@@ -1260,10 +1260,6 @@
         return true;
     }
 
-    public Map getServerInstanceProperties() {
-        return getRuntimeDelegate().getServerInstanceProperties();
-    }
-
     protected GeronimoRuntimeDelegate getRuntimeDelegate() {
         GeronimoRuntimeDelegate rd = (GeronimoRuntimeDelegate) getServer().getRuntime().getAdapter(GeronimoRuntimeDelegate.class);
         if (rd == null)
diff --git a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerDelegate.java b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerDelegate.java
index b7e296d..f78cdce 100644
--- a/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerDelegate.java
+++ b/plugins/org.apache.geronimo.st.v30.core/src/main/java/org/apache/geronimo/st/v30/core/GeronimoServerDelegate.java
@@ -40,7 +40,6 @@
 import org.apache.geronimo.st.v30.core.internal.Trace;
 import org.apache.geronimo.st.v30.core.osgi.AriesHelper;
 import org.apache.geronimo.st.v30.core.osgi.OsgiConstants;
-import org.apache.geronimo.st.v30.core.util.ConfigSubstitutionsHelper;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -53,7 +52,6 @@
 import org.eclipse.wst.common.componentcore.internal.util.IModuleConstants;
 import org.eclipse.wst.server.core.IModule;
 import org.eclipse.wst.server.core.IModuleType;
-import org.eclipse.wst.server.core.IRuntime;
 import org.eclipse.wst.server.core.IServer;
 import org.eclipse.wst.server.core.ServerPort;
 import org.eclipse.wst.server.core.ServerUtil;
@@ -566,43 +564,14 @@
         setRunFromWorkspace(false);
         setSelectClasspathContainers(false);
         
-        IServer server = getServer();
-        if (server != null) {
-            IRuntime runtime = server.getRuntime();
-            if (runtime != null) {
-                ConfigSubstitutionsHelper configSubstitutions = new ConfigSubstitutionsHelper(runtime.getLocation());
-                configSubstitutions.load();
-                setAttribute(configSubstitutions, ConfigSubstitutionsHelper.PORT_OFFSET, PROPERTY_PORT_OFFSET);
-                setAttribute(configSubstitutions, ConfigSubstitutionsHelper.HTTP_PORT, PROPERTY_HTTP_PORT);
-                setAttribute(configSubstitutions, ConfigSubstitutionsHelper.NAMING_PORT, PROPERTY_RMI_PORT);
-            }
-        }
-
         resumeArgUpdates();
         Trace.tracePoint("Exit", Activator.traceCore, "GeronimoServerDelegate.setDefaults", monitor);
     }
     
-    private void setAttribute(ConfigSubstitutionsHelper configSubstitutions, String substProperty, String property) {
-        String value = configSubstitutions.getProperty(substProperty);
-        if (value != null) {
-            setAttribute(property, value);
-        }
-    }
-
     @Override
     public void saveConfiguration(IProgressMonitor monitor) throws CoreException {
         Trace.tracePoint("Enter", Activator.traceCore, "GeronimoServerDelegate.saveConfiguration", monitor);
         super.saveConfiguration(monitor);
-        
-        if (SocketUtil.isLocalhost(getServer().getHost())) {
-            ConfigSubstitutionsHelper configSubstitutions = new ConfigSubstitutionsHelper(getServer().getRuntime().getLocation());
-            configSubstitutions.load();
-            configSubstitutions.setProperty(ConfigSubstitutionsHelper.PORT_OFFSET, String.valueOf(getPortOffset()));
-            configSubstitutions.setProperty(ConfigSubstitutionsHelper.HTTP_PORT, getHTTPPort());
-            configSubstitutions.setProperty(ConfigSubstitutionsHelper.NAMING_PORT, getRMINamingPort());
-            configSubstitutions.store();            
-        }
-
         Trace.tracePoint("Exit", Activator.traceCore, "GeronimoServerDelegate.saveConfiguration", monitor);
     }
     
diff --git a/plugins/org.apache.geronimo.st.v30.ui/src/main/java/org/apache/geronimo/st/v30/ui/internal/GeronimoRuntimeWizardFragment.java b/plugins/org.apache.geronimo.st.v30.ui/src/main/java/org/apache/geronimo/st/v30/ui/internal/GeronimoRuntimeWizardFragment.java
index 8a8f7b2..cae2e53 100644
--- a/plugins/org.apache.geronimo.st.v30.ui/src/main/java/org/apache/geronimo/st/v30/ui/internal/GeronimoRuntimeWizardFragment.java
+++ b/plugins/org.apache.geronimo.st.v30.ui/src/main/java/org/apache/geronimo/st/v30/ui/internal/GeronimoRuntimeWizardFragment.java
@@ -317,7 +317,6 @@
         }
 
         IRuntimeWorkingCopy runtimeWC = getRuntimeDelegate().getRuntimeWorkingCopy();
-        getRuntimeDelegate().setInstanceProperty("serverRootDirectory", installDir.getText());
 
         if (installDir.getText() == null || installDir.getText().length() == 0) {
             // installDir field has not been entered